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- PDB-4fnd: Crystal structure of the Mtb enoyl CoA isomerase in complex with ... -

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Basic information

Entry
Database: PDB / ID: 4fnd
TitleCrystal structure of the Mtb enoyl CoA isomerase in complex with hydroxyhexanoyl CoA
ComponentsEnoyl-CoA hydratase/isomerase family protein
KeywordsISOMERASE / Structural Genomics / TB Structural Genomics Consortium / TBSGC / crotonase superfamily
Function / homology
Function and homology information


enoyl-CoA hydratase / enoyl-CoA hydratase activity / plasma membrane / cytosol
Similarity search - Function
Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / 2-enoyl-CoA Hydratase; Chain A, domain 1 / 2-enoyl-CoA Hydratase; Chain A, domain 1 / ClpP/crotonase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
(S)-3-Hydroxyhexanoyl-CoA / Enoyl-CoA hydratase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsBruning, J.B. / Gao, N. / Hernandez, E.D. / Li, H. / Dang, N. / Hung, L.W. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: To be Published
Title: Crystal structure and mechanism of the prokaryotic enoyl CoA isomerase
Authors: Bruning, J.B. / Gao, N. / Hernandez, E.D. / Li, H. / Dang, N. / Hung, L.W. / Moran, S. / Sacchettini, J.C.
History
DepositionJun 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5374
Polymers24,4671
Non-polymers1,0703
Water5,170287
1
A: Enoyl-CoA hydratase/isomerase family protein
hetero molecules

A: Enoyl-CoA hydratase/isomerase family protein
hetero molecules

A: Enoyl-CoA hydratase/isomerase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,61012
Polymers73,4013
Non-polymers3,2099
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area6820 Å2
ΔGint-131 kcal/mol
Surface area24530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.018, 77.018, 135.595
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

21A-302-

SO4

31A-303-

SO4

41A-303-

SO4

51A-567-

HOH

61A-654-

HOH

71A-662-

HOH

81A-665-

HOH

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Components

#1: Protein Enoyl-CoA hydratase/isomerase family protein / Enoyl-coA hydratase homolog / PROBABLE ENOYL-CoA HYDRATASE ECHA3 (ENOYL HYDRASE) (UNSATURATED ACYL- ...Enoyl-coA hydratase homolog / PROBABLE ENOYL-CoA HYDRATASE ECHA3 (ENOYL HYDRASE) (UNSATURATED ACYL-CoA HYDRATASE) (CROTONASE)


Mass: 24466.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: echA3, MT0660, Rv0632c / Plasmid: pvp16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96907, enoyl-CoA hydratase
#2: Chemical ChemComp-3H9 / (S)-3-Hydroxyhexanoyl-CoA


Mass: 877.645 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H42N7O18P3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.2M ammonium sulfate, 0.1M HEPES 7.0, and 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 14, 2010 / Details: mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 9.4 % / Number: 199021 / Rmerge(I) obs: 0.076 / Χ2: 0.96 / D res high: 1.85 Å / D res low: 47.55 Å / Num. obs: 21023 / % possible obs: 99.9
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
3.9947.5599.70.0360.768.95582
3.163.9999.60.0520.799.36357
2.763.161000.0820.879.72139
2.512.7699.90.1220.969.74170
2.332.511000.1560.979.7362
2.192.331000.19419.6169
2.082.191000.2541.039.5538
1.992.081000.3231.089.4534
1.921.991000.3881.19.3825
1.851.921000.4551.078.517
ReflectionResolution: 1.85→47.55 Å / Num. all: 21023 / Num. obs: 21023 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 29.07 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Χ2: 0.96 / Net I/σ(I): 12.4 / Scaling rejects: 1493
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.85-1.928.50.4553.61744420501.07100
1.92-1.999.380.3884.31920620441.1100
1.99-2.089.450.3234.91953720641.08100
2.08-2.199.550.25461967120551.03100
2.19-2.339.610.1947.32004220791100
2.33-2.519.730.1568.82016120660.97100
2.51-2.769.740.12210.82062621010.9699.9
2.76-3.169.720.08216.42057721020.87100
3.16-3.999.360.05224.42048121510.7999.6
3.99-47.558.950.03634.52127623110.7699.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
d*TREK9.9Ldata reduction
PHASERphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FN7 chain A

4fn7


Resolution: 1.85→38.509 Å / Occupancy max: 1 / Occupancy min: 0.16 / FOM work R set: 0.8488 / SU ML: 0.31 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 21.17 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 1073 5.12 %random
Rwork0.1957 ---
all0.1979 20968 --
obs0.1979 20968 99.65 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.512 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso max: 75.99 Å2 / Biso mean: 29.4781 Å2 / Biso min: 16.04 Å2
Baniso -1Baniso -2Baniso -3
1-4.2371 Å20 Å2-0 Å2
2--4.2371 Å2-0 Å2
3----8.4741 Å2
Refinement stepCycle: LAST / Resolution: 1.85→38.509 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 66 287 2057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061834
X-RAY DIFFRACTIONf_angle_d0.9852499
X-RAY DIFFRACTIONf_chiral_restr0.063284
X-RAY DIFFRACTIONf_plane_restr0.004322
X-RAY DIFFRACTIONf_dihedral_angle_d19.472709
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.93420.29591330.250224212554100
1.9342-2.03620.32161390.225724132552100
2.0362-2.16370.28741320.21224532585100
2.1637-2.33080.27781290.20724532582100
2.3308-2.56530.26981400.206224582598100
2.5653-2.93640.26661320.198824782610100
2.9364-3.6990.20261310.185625312662100
3.699-38.51730.21661370.18262688282599

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